[phenixbb] sculptor : "Wrong alignment format:"

[Dr G. Bunkoczi]

Hi Bryan,

>i finally understand that sculptor is in fact calculating an
>alignment. my alignments have been pre-aligned (mafft usually). i have
>not tried a .def to turn off the alignment - can i do that?

Sculptor has to match your protein model with your alignment. For all other 
calculations, Sculptor uses the alignment you provide. You can also ask 
Sculptor to create this alignment for you (it is off by default).

>in terms of algorithms out there, IIUC mafft has a very sophisticated
>algorithm for it, and at any rate it can be compiled with
>multithreading. its license appears not to be prohibitive.

I will have a look at MAFFT, but I do hope the speed issues will disappear 
with the new version (you may have to wait till tomorrow, as I have 
literally checked in the changes a couple of hours ago).

BW, Gabor